6 ms·

There is at least one thing wrong about this. This is an essay about a paper published a simulation based scenarios in medical research. It then try to generali

There is at least one thing wrong about this. This is an essay about a paper published a simulation based scenarios in medical research. It then try to generalize to "research" and avoid this very narrow support to the claim. I think this is something true and it should make us more cautious when deciding based on single studies. But things are different in other fields. Also this is called research. You don't know the answer before head. You have limitations in tech and tools you use. You might miss something, didn't have access to more information that could change the outcome. That is why research is a process. Unfortunately common science books talks only about discoveries, results that are considered fact but usually don't do much about the history of how we got there. I would like to suggest a great book called "How experiments end"[1] and enjoy going into details on how scientific conscious is built for many experiments in different fields (mostly physics). [1] https://press.uchicago.edu/ucp/books/book/chicago/H/bo5969426.html https://press.uchicago.edu/ucp/books/book/chicago/H/bo596942...

thatguysaguy 2y ago
I think it's clear that this paper has stood the rest of time over the last 20 years. Our estimates of how much published work fails to replicate or is outright fraudulent have only increased since then.
- tptacek 2y ago
  Outright research fraud is probably very rare; the cases we've heard about stick out, but people outside of academia usually don't have a good intuition for just how vast the annual output of the sciences are. Remember the famous PhD comic, showing how your thesis is going to be an infinitesimal fraction of the work of your field.
  - dekhn 2y ago
    Is incompetence fraud? Or just incompetence? I'm asking because a fair number of the molecular biologists who get caught by Elizabeth Bik for copy/pasting images of gels insist they just made honest mistakes (with some commentary about the atrocious nature of record-keeping in modern biology). I alter Ionnides's conclusion to be instead: "Roughly 50% of papers in quantitative biological sciences contain at least one error serious enough to invalidate the conclusion" and "Roughly 75% of really interesting papers are missing at least one load-bearing method detail that reproducers must figure out on their own" (my own personal observations of the literature are consistent with these rates; I was always flabbergasted at people who just took Figure 3 as correct).
    - kelipso 2y ago
      There is no one hovering over scientists all the time ready to stick a hot poker in them when they make a mistake or get careless. I was in academia and my impression is there is a reluctance to double and triple check results to make sure they are right as long as the results match your instincts, whether it's time pressure, laziness, bias, or just being human.
      - dekhn 2y ago
        At least in my own mental model of publishing a paper (I've published only a few), I'd want my coauthors to stick hot pokers in my if I made a mistake or got careless. But then, my entire thesis was driven by a reproducible Makefile that downloaded the latest results from a supercomputer, re-ran the whole analysis, and wrote the latex necessary (at least partly to avoid making trivial mistakes). It was clear everything I was doing was just getting in the way of publishing high prestige papers.
        robwwilliams 2y ago
        All too easy to understand your situation. NIH is finally but slowly waking up and is imposing more “onerous” (aka: essential and correct) data management and sharing (DMS) document. Every grant applicant now submits following these guidelines: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-24-175.html https://grants.nih.gov/grants/guide/notice-files/NOT-OD-24-1... Unfortunately, not all NIH institutes understand how to evaluate and moderate this key new policy. Oddly enough the peer reviewers do NOT have access to DMS plans as of this year.
        IG_Semmelweiss 2y ago
        Is this a process whereby the researcher is forced to submit the thesis (null, etc) of the research, ahead of the study and its findings?
        robwwilliams 2y ago
  - kelipso 2y ago
    Research fraud is likely very rare but it's not about a few stories that show up about unreplicable studies that stick out. There was a study a few years where they tried to replicate a bunch of top cited psychology papers and the majority of the experiments were not replicated. Then people did the same for other disciplines afterwards and, while it wasn't as bad as psychology, there were plenty of papers they couldn't replicate.
    - tptacek 2y ago
      Every time this topic comes up I'm reminded of what Stefan Savage, a hero of mine, said about academic papers ("studies", in the sense we're discussing here): they are the beginnings of conversations, not the end. It shouldn't shock people that results in papers might not replicate; papers aren't infallible, which makes sense when you consider the process that produces them.
      - robwwilliams 2y ago
        That is a generous interpretation. But in many cases we try our best to dress up studies and tell good stories—-preferably stories with compelling positive statistics and with slick figures. The story telling often obscures the key data.
        mrguyorama 2y ago
        No, "Science" "Journalists" who have zero scientific training will take an extremely limited study and completely miss the point and make wild claims that the general population becomes convinced the "science" said. Scientists do not consider a study to be more than an observation. What matters to scientists is the totality of the evidence. There are several chemistry youtubers who have failed to "reproduce" papers they are working from. Does that mean chemistry is a farce and doesn't work? No, it means some chemist at some point in history failed to write something down, mostly because they didn't even know or realize it mattered. Science is incredibly difficult and we can only hope to be okay at it.
        2y ago
  - jklinger410 2y ago
    > Outright research fraud is probably very rare Not sure what rare means in this context. The more important research is, the more likely there is fraud involved. So in terms of size of impact, it's probably very common. And then if you combine this with poorly done, non repeatable, or inconclusive research being parroted as a discovery...You end up with quite a bit of BS research.
- giantg2 2y ago
  [Please consider the following with an open mind] Just because a study doesn't replicate, doesn't make it false. This is especially true in medicine where the potential global subjects/population are very diverse. You can do a small study that suggests further research based on a small sample size, or even a case study. The next study might have a conflicting finding, but that doesn't make the first one false - rather a step in the overall process of gaining new information.
  - llamaimperative 2y ago
    I think it's much, much more powerful to think of "failure to replicate" as "failure to generalize." In lieu of actual fraud or a methodological mistake that wasn't represented/caught in peer review, it's still extremely difficult to control for all possible sources of variation. That's especially true as you go further "up the stack" from math -> physics -> chem -> bio -> psych -> social. It is absolutely possible to honestly conduct a very high quality experiment with a real finding, but fail to account for something like "on the way here, 80% of participants encountered a frustrating traffic jam." Their finding could be true for people who just encountered a traffic jam, and lack of replication would be due to an unsuccessful generalization from what they found.
    - scns 2y ago
      Dislike being a pedant but the stack was missing math up front
      - llamaimperative 2y ago
        Haha, math strikes me as a bit different from the others... but I'll add it just for you ;)
        gopher_space 2y ago
        Dislike being a pedant but the stack is missing philosophy up front.
      - 2y ago
a_bonobo 2y ago
I remember criticism back from when this paper first came out: it went something like 'all this shows that using maths it is possible to construct a world where most published research findings are false.'
ants_everywhere 2y ago
I think the best way to view this paper is as a sort of meta-analysis of a wider literature around null hypothesis testing and p-values. That literature goes back at least to the 1970s with the work of people like Paul Meehl and Gene Glass. But you can push it further back, like the 1957 Lindley Paradox that Ioannidis cites. Part of the reason this paper was impactful is that it was short and punchy, took aim at all of medicine rather than a smaller subfield, and didn't require as much mathematical understanding as other papers. I knew some of the big names that were hit by the replication crisis. And before that I spent some time trying to talk to psychology researchers at a top school about the problems with statistical testing. But they had limited knowledge of stats and didn't want to go out on a limb when everyone else in the field seemed okay with the status quo. A paper like this can be read by everyone and makes a forceful argument. > It then try to generalize to "research" and avoid this very narrow support to the claim This is a good point. The methods in medicine and the social sciences are especially weak and prone to these sorts of criticisms. In the physical sciences, often you can run enough iterations of the experiment to overwhelm any prior. > You have limitations in tech and tools you use. You might miss something, didn't have access to more information that could change the outcome. That is why research is a process. I totally agree. Science is basically a control system, or a root finding algorithm, or gradient descent. At any time t there is a gap between the best known science and the truth. But the point is that science converges to the truth over time, whereas no other alternative does.
- verisimi 2y ago
  The scientific method converges on the truth. But science need not. If the foundational assumptions are wrong or impossible to challenge, time t can extend indefinitely. Additionally, it is surely possible that whole sections of science is waylaid and diverges from truth on account of funding, legislation, big personalities, etc.
  - DrNosferatu 2y ago
    But what is “truth”?
    - 2y ago
throwoutway 2y ago
> But things are different in other fields. Everyone claims its different in their field
- singleshot_ 2y ago
  Strangely, we don't in my field!
InDubioProRubio 2y ago
Could one filter for the true research, by searching for "outliers" which are not outliars, aka data that does not fit the ruling narrative, but at the same time has no narrative of its own?
veunes 2y ago
> Unfortunately common science books talks only about discoveries, results that are considered fact but usually don't do much about the history of how we got there. The journey to discovery is often just as fascinating as the results themselves. The process (the false starts, debates, even the dead ends) can be incredibly instructive and inspiring.
- SkyBelow 2y ago
  It is also key to building the idea that we don't have truth, we have the best model we have so far not found reason to reject (and sometimes one that is rejected as truth, but useful for some problems to be kept around). I see too many people, haven taken some science classes, feel that they know what the 'truth' of the universe is, which locks down their ability to question and break current models in search of newer, even better, models.
dumb1224 2y ago
It is a bit of Russells paradox isn't it :D If this is research then it shouldn't be true as it should belong to the 'most' research set.

thatguysaguy 2y ago

I think it's clear that this paper has stood the rest of time over the last 20 years. Our estimates of how much published work fails to replicate or is outright fraudulent have only increased since then.

tptacek 2y ago
Outright research fraud is probably very rare; the cases we've heard about stick out, but people outside of academia usually don't have a good intuition for just how vast the annual output of the sciences are. Remember the famous PhD comic, showing how your thesis is going to be an infinitesimal fraction of the work of your field.
- dekhn 2y ago
  Is incompetence fraud? Or just incompetence? I'm asking because a fair number of the molecular biologists who get caught by Elizabeth Bik for copy/pasting images of gels insist they just made honest mistakes (with some commentary about the atrocious nature of record-keeping in modern biology). I alter Ionnides's conclusion to be instead: "Roughly 50% of papers in quantitative biological sciences contain at least one error serious enough to invalidate the conclusion" and "Roughly 75% of really interesting papers are missing at least one load-bearing method detail that reproducers must figure out on their own" (my own personal observations of the literature are consistent with these rates; I was always flabbergasted at people who just took Figure 3 as correct).
  - kelipso 2y ago
    There is no one hovering over scientists all the time ready to stick a hot poker in them when they make a mistake or get careless. I was in academia and my impression is there is a reluctance to double and triple check results to make sure they are right as long as the results match your instincts, whether it's time pressure, laziness, bias, or just being human.
    - dekhn 2y ago
      At least in my own mental model of publishing a paper (I've published only a few), I'd want my coauthors to stick hot pokers in my if I made a mistake or got careless. But then, my entire thesis was driven by a reproducible Makefile that downloaded the latest results from a supercomputer, re-ran the whole analysis, and wrote the latex necessary (at least partly to avoid making trivial mistakes). It was clear everything I was doing was just getting in the way of publishing high prestige papers.
      - robwwilliams 2y ago
        All too easy to understand your situation. NIH is finally but slowly waking up and is imposing more “onerous” (aka: essential and correct) data management and sharing (DMS) document. Every grant applicant now submits following these guidelines: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-24-175.html https://grants.nih.gov/grants/guide/notice-files/NOT-OD-24-1... Unfortunately, not all NIH institutes understand how to evaluate and moderate this key new policy. Oddly enough the peer reviewers do NOT have access to DMS plans as of this year.
        IG_Semmelweiss 2y ago
        Is this a process whereby the researcher is forced to submit the thesis (null, etc) of the research, ahead of the study and its findings?
        robwwilliams 2y ago
- kelipso 2y ago
  Research fraud is likely very rare but it's not about a few stories that show up about unreplicable studies that stick out. There was a study a few years where they tried to replicate a bunch of top cited psychology papers and the majority of the experiments were not replicated. Then people did the same for other disciplines afterwards and, while it wasn't as bad as psychology, there were plenty of papers they couldn't replicate.
  - tptacek 2y ago
    Every time this topic comes up I'm reminded of what Stefan Savage, a hero of mine, said about academic papers ("studies", in the sense we're discussing here): they are the beginnings of conversations, not the end. It shouldn't shock people that results in papers might not replicate; papers aren't infallible, which makes sense when you consider the process that produces them.
    - robwwilliams 2y ago
      That is a generous interpretation. But in many cases we try our best to dress up studies and tell good stories—-preferably stories with compelling positive statistics and with slick figures. The story telling often obscures the key data.
      - mrguyorama 2y ago
        No, "Science" "Journalists" who have zero scientific training will take an extremely limited study and completely miss the point and make wild claims that the general population becomes convinced the "science" said. Scientists do not consider a study to be more than an observation. What matters to scientists is the totality of the evidence. There are several chemistry youtubers who have failed to "reproduce" papers they are working from. Does that mean chemistry is a farce and doesn't work? No, it means some chemist at some point in history failed to write something down, mostly because they didn't even know or realize it mattered. Science is incredibly difficult and we can only hope to be okay at it.
        2y ago
- jklinger410 2y ago
  > Outright research fraud is probably very rare Not sure what rare means in this context. The more important research is, the more likely there is fraud involved. So in terms of size of impact, it's probably very common. And then if you combine this with poorly done, non repeatable, or inconclusive research being parroted as a discovery...You end up with quite a bit of BS research.
giantg2 2y ago
[Please consider the following with an open mind] Just because a study doesn't replicate, doesn't make it false. This is especially true in medicine where the potential global subjects/population are very diverse. You can do a small study that suggests further research based on a small sample size, or even a case study. The next study might have a conflicting finding, but that doesn't make the first one false - rather a step in the overall process of gaining new information.
- llamaimperative 2y ago
  I think it's much, much more powerful to think of "failure to replicate" as "failure to generalize." In lieu of actual fraud or a methodological mistake that wasn't represented/caught in peer review, it's still extremely difficult to control for all possible sources of variation. That's especially true as you go further "up the stack" from math -> physics -> chem -> bio -> psych -> social. It is absolutely possible to honestly conduct a very high quality experiment with a real finding, but fail to account for something like "on the way here, 80% of participants encountered a frustrating traffic jam." Their finding could be true for people who just encountered a traffic jam, and lack of replication would be due to an unsuccessful generalization from what they found.
  - scns 2y ago
    Dislike being a pedant but the stack was missing math up front
    - llamaimperative 2y ago
      Haha, math strikes me as a bit different from the others... but I'll add it just for you ;)
      - gopher_space 2y ago
        Dislike being a pedant but the stack is missing philosophy up front.
    - 2y ago

a_bonobo 2y ago

I remember criticism back from when this paper first came out: it went something like 'all this shows that using maths it is possible to construct a world where most published research findings are false.'

ants_everywhere 2y ago

I think the best way to view this paper is as a sort of meta-analysis of a wider literature around null hypothesis testing and p-values. That literature goes back at least to the 1970s with the work of people like Paul Meehl and Gene Glass. But you can push it further back, like the 1957 Lindley Paradox that Ioannidis cites. Part of the reason this paper was impactful is that it was short and punchy, took aim at all of medicine rather than a smaller subfield, and didn't require as much mathematical understanding as other papers. I knew some of the big names that were hit by the replication crisis. And before that I spent some time trying to talk to psychology researchers at a top school about the problems with statistical testing. But they had limited knowledge of stats and didn't want to go out on a limb when everyone else in the field seemed okay with the status quo. A paper like this can be read by everyone and makes a forceful argument. > It then try to generalize to "research" and avoid this very narrow support to the claim This is a good point. The methods in medicine and the social sciences are especially weak and prone to these sorts of criticisms. In the physical sciences, often you can run enough iterations of the experiment to overwhelm any prior. > You have limitations in tech and tools you use. You might miss something, didn't have access to more information that could change the outcome. That is why research is a process. I totally agree. Science is basically a control system, or a root finding algorithm, or gradient descent. At any time t there is a gap between the best known science and the truth. But the point is that science converges to the truth over time, whereas no other alternative does.

verisimi 2y ago
The scientific method converges on the truth. But science need not. If the foundational assumptions are wrong or impossible to challenge, time t can extend indefinitely. Additionally, it is surely possible that whole sections of science is waylaid and diverges from truth on account of funding, legislation, big personalities, etc.
- DrNosferatu 2y ago
  But what is “truth”?
  - 2y ago

throwoutway 2y ago

> But things are different in other fields. Everyone claims its different in their field

singleshot_ 2y ago
Strangely, we don't in my field!

InDubioProRubio 2y ago

Could one filter for the true research, by searching for "outliers" which are not outliars, aka data that does not fit the ruling narrative, but at the same time has no narrative of its own?

veunes 2y ago

> Unfortunately common science books talks only about discoveries, results that are considered fact but usually don't do much about the history of how we got there. The journey to discovery is often just as fascinating as the results themselves. The process (the false starts, debates, even the dead ends) can be incredibly instructive and inspiring.

SkyBelow 2y ago
It is also key to building the idea that we don't have truth, we have the best model we have so far not found reason to reject (and sometimes one that is rejected as truth, but useful for some problems to be kept around). I see too many people, haven taken some science classes, feel that they know what the 'truth' of the universe is, which locks down their ability to question and break current models in search of newer, even better, models.

dumb1224 2y ago

It is a bit of Russells paradox isn't it :D If this is research then it shouldn't be true as it should belong to the 'most' research set.